D. Branduardi

发表

The role of the peripheral anionic site and cation-pi interactions in the ligand penetration of the human AChE gorge.

Francesco Luigi Gervasio, Michele Parrinello, Maurizio Recanatini, 2005, Journal of the American Chemical Society.

Metadynamics with Adaptive Gaussians.

M. Parrinello, G. Bussi, D. Branduardi, 2012, Journal of chemical theory and computation.

The unfolded ensemble and folding mechanism of the C-terminal GB1 beta-hairpin.

M. Parrinello, F. Gervasio, M. Bonomi, 2008, Journal of the American Chemical Society.

Protein conformational transitions: the closure mechanism of a kinase explored by atomistic simulations.

A. Cavalli, M. Parrinello, M. Recanatini, 2009, Journal of the American Chemical Society.

Cytostatic and cytotoxic effects of topotecan decoded by a novel mathematical simulation approach.

Paolo Ubezio, Monica Lupi, Davide Branduardi, 2004, Cancer research.

Discovery of a new class of highly potent inhibitors of acid ceramidase: synthesis and structure-activity relationship (SAR).

G. Bottegoni, M. Mor, D. Piomelli, 2013, Journal of medicinal chemistry.

Theoretical insights into the mechanism of carbon monoxide (CO) release from CO-releasing molecules.

A. Cavalli, Matteo Masetti, Sai V. C. Vummaleti, 2012, Chemistry.

Funnel-Metadynamics 2 . 0 Graphic user interface and implementation in Plumed

V. Limongelli, D. Branduardi, S. Raniolo, 2022 .

Covalent inhibitors of fatty acid amide hydrolase: a rationale for the activity of piperidine and piperazine aryl ureas.

A. Cavalli, M. Mor, D. Piomelli, 2011, Journal of medicinal chemistry.

PLUMED 2: New feathers for an old bird

Massimiliano Bonomi, Gareth A. Tribello, Davide Branduardi, 2013, Comput. Phys. Commun..

String method for calculation of minimum free-energy paths in Cartesian space in freely-tumbling systems.

Davide Branduardi, José D Faraldo-Gómez, J. Faraldo-Gómez, 2013, Journal of chemical theory and computation.

Promoting transparency and reproducibility in enhanced molecular simulations

Jakub Rydzewski, Toni Giorgino, Massimiliano Bonomi, 2019, Nature Methods.

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

Massimiliano Bonomi, Davide Provasi, Michele Parrinello, 2009, Comput. Phys. Commun..

Insights into Ligand–Protein Binding from Local Mechanical Response

Matteo Masetti, Walter Rocchia, Andrea Cavalli, 2011, Journal of chemical theory and computation.

From A to B in free energy space.

Francesco Luigi Gervasio, Michele Parrinello, Davide Branduardi, 2007, The Journal of chemical physics.

A chirality‐based metrics for free‐energy calculations in biomolecular systems

Massimiliano Bonomi, Michele Parrinello, Davide Branduardi, 2011, J. Comput. Chem..

Investigating the mechanism of substrate uptake and release in the glutamate transporter homologue Glt(Ph) through metadynamics simulations.

Michele Parrinello, Ettore Novellino, Giovanni Grazioso, 2012, Journal of the American Chemical Society.

Binding sites for SiH2/Si(001) : A combined ab initio, tight-binding, and classical investigation

L. Miglio, D. Branduardi, F. Montalenti, 2006 .

Quantitative assessment of the complex dynamics of G1, S, and G2-M checkpoint activities.

Paolo Ubezio, Monica Lupi, Valentina Colombo, 2009, Cancer research.

Nucleotide-dependent conformational states of actin

Jim Pfaendtner, Gregory A Voth, Michele Parrinello, 2009, Proceedings of the National Academy of Sciences.

A Catalytic Mechanism for Cysteine N-Terminal Nucleophile Hydrolases, as Revealed by Free Energy Simulations

A. Cavalli, M. Mor, D. Piomelli, 2012, PloS one.

Free‐Energy Calculations with Metadynamics: Theory and Practice

Giovanni Bussi, Davide Branduardi, G. Bussi, 2015 .

Conformational changes and gating at the selectivity filter of potassium channels.

Francesco L Gervasio, Michele Parrinello, Carmen Domene, 2008, Journal of the American Chemical Society.

The role of Li+, Na+, and K+ in the ligand binding inside the human acetylcholinesterase gorge

Francesco Luigi Gervasio, Michele Parrinello, Maurizio Recanatini, 2008, Proteins.

Atomic‐resolution dissection of the energetics and mechanism of isomerization of hydrated ATP‐Mg2+ through the SOMA string method

Davide Branduardi, José D. Faraldo-Gómez, Fabrizio Marinelli, 2016, J. Comput. Chem..

Investigating the mechanism of substrate uptake and release in the glutamate transporter homologue Glt(Ph) through metadynamics simulations.

A. Cavalli, M. Parrinello, E. Novellino, 2012, Journal of the American Chemical Society.

Quantitative assessment of the complex dynamics of G1, S, and G2-M checkpoint activities.

M. Lupi, G. Matera, C. Natoli, 2009, Cancer research.

Free-energy-based methods for binding profile determination in a congeneric series of CDK2 inhibitors.

F. Gervasio, Jérémy Fidelak, J. Juraszek, 2010, Journal of Physical Chemistry B.